Contacts of the helix formed by residues 79 - 96 (chain A) in PDB entry 3SRH
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 79 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A GLY* 1.3 74.1 - - - -
80A HIS* 1.3 68.0 + - - +
81A GLU* 3.7 8.1 + - - +
82A TYR* 3.4 20.9 + - - +
83A HIS* 3.1 27.1 + - - -
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Residues in contact with HIS 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A PHE* 4.5 11.2 - + - -
78A GLY 5.2 2.0 - - - -
79A THR* 1.3 76.2 - - - +
81A GLU* 1.3 60.0 + - - +
83A HIS* 3.5 1.5 + - - -
84A ALA* 2.9 32.3 + - - +
223A LYS* 5.2 2.7 + - - -
226A GLN* 4.0 17.9 + - + +
227A ASP* 2.8 28.4 + - - -
230A PHE* 3.3 52.5 - + + +
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Residues in contact with GLU 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A THR* 3.7 7.1 + - - +
80A HIS* 1.3 78.3 - - - +
82A TYR* 1.3 62.7 + - - +
84A ALA* 3.3 6.0 + - - +
85A GLU* 3.1 28.0 + - + +
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Residues in contact with TYR 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ILE 5.8 1.1 - - - -
51A GLY* 5.4 5.4 - - - -
52A PRO* 3.8 29.6 - - + +
55A ARG* 3.4 54.8 + - - +
78A GLY* 4.7 13.7 - - - -
79A THR* 3.4 24.2 + - - +
80A HIS 3.3 0.2 - - - -
81A GLU* 1.3 79.8 - - - +
83A HIS* 1.3 71.2 + + - +
85A GLU* 3.5 4.8 + - - +
86A THR* 2.9 29.0 + - - -
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Residues in contact with HIS 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ILE 5.7 4.0 - - - -
73A LEU* 3.3 28.9 - - + +
74A ASN 3.5 20.8 + - - -
75A PHE* 3.8 38.5 - + + -
77A HIS 2.9 22.2 + - - -
78A GLY* 3.7 12.4 - - - -
79A THR 3.1 23.2 + - - +
80A HIS* 4.0 3.1 - + - +
82A TYR* 1.3 87.3 - + - +
84A ALA* 1.3 60.0 + - - +
86A THR* 3.2 8.1 + - - +
87A ILE* 3.0 33.6 + - - +
230A PHE* 4.3 5.2 - - + -
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Residues in contact with ALA 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A HIS 2.9 19.8 + - - +
81A GLU* 3.7 6.5 - - - +
83A HIS* 1.3 75.8 - - - +
85A GLU* 1.3 58.4 + - - +
87A ILE* 3.4 3.3 + - - +
88A LYS* 2.9 27.8 + - - +
230A PHE* 4.0 10.3 - - + -
234A GLN* 3.8 26.1 - - - +
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Residues in contact with GLU 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ARG* 2.9 26.7 + - - +
81A GLU* 3.1 20.5 + - + +
82A TYR* 3.7 5.0 - - - +
83A HIS 3.3 0.2 - - - -
84A ALA* 1.3 72.9 - - - +
86A THR* 1.3 55.9 - - - +
88A LYS* 3.3 17.7 + - - +
89A ASN* 2.7 57.1 + - - +
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Residues in contact with THR 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ILE* 3.7 39.7 - - + +
55A ARG* 3.0 28.5 + - + +
60A LEU* 4.6 0.4 - - + +
73A LEU* 4.3 16.8 - - + -
82A TYR* 2.9 19.5 + - - -
83A HIS* 3.4 13.7 + - - +
85A GLU* 1.3 78.5 - - - +
87A ILE* 1.3 52.3 + - - +
89A ASN* 3.3 7.1 + - - +
90A VAL* 2.8 34.8 + - + +
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Residues in contact with ILE 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A LEU* 3.7 22.2 - - + -
75A PHE* 5.6 1.3 - - + -
83A HIS 3.0 20.0 + - - +
84A ALA 3.7 4.5 - - - +
85A GLU 3.2 0.2 - - - -
86A THR* 1.3 73.2 - - - +
88A LYS* 1.3 61.8 + - - +
90A VAL* 3.4 7.2 + - - +
91A ARG* 3.0 67.6 + - - +
109A VAL* 4.2 23.6 - - + -
111A LEU* 6.5 0.2 - - + -
230A PHE* 4.4 12.6 - - + -
234A GLN* 4.0 31.4 - - + +
236A VAL* 4.7 5.2 - - + -
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Residues in contact with LYS 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A ALA 2.9 18.1 + - - +
85A GLU* 3.4 17.7 - - - +
87A ILE* 1.3 77.5 - - - +
89A ASN* 1.3 64.7 + - - +
91A ARG* 3.3 7.2 + - + +
92A THR* 2.9 42.6 + - - +
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Residues in contact with ASN 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ARG* 3.3 35.8 + - - +
56A SER* 4.3 4.2 - - - +
57A VAL* 3.5 29.4 - - + +
60A LEU* 3.7 4.1 - - + +
85A GLU* 2.7 44.1 + - - +
86A THR 3.6 4.9 - - - +
88A LYS* 1.3 80.9 + - - +
90A VAL* 1.3 64.1 + - - +
92A THR* 4.4 1.3 + - - -
93A ALA* 3.1 24.6 + - - +
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Residues in contact with VAL 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ILE* 4.6 6.1 - - + -
60A LEU* 3.8 26.7 - - + -
64A ILE* 4.9 0.6 - - + +
68A MET* 5.4 2.0 - - + -
71A ALA* 4.0 20.6 - - + -
73A LEU* 5.6 2.0 - - + -
86A THR* 2.8 27.1 + - + +
87A ILE* 3.7 7.6 - - - +
88A LYS 3.4 0.2 - - - -
89A ASN* 1.3 72.0 - - - +
91A ARG* 1.3 55.6 + - + +
93A ALA* 3.3 4.2 + - - +
94A THR* 2.7 50.0 + - - +
107A VAL* 4.3 16.6 - - + +
109A VAL* 4.3 23.1 - - + -
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Residues in contact with ARG 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A ILE* 3.0 43.3 + - - +
88A LYS* 3.7 6.5 - - - +
90A VAL* 1.3 77.4 - - + +
92A THR* 1.3 56.9 + - - +
94A THR* 4.3 5.8 - - - -
95A GLU* 2.7 49.0 + - + +
109A VAL* 4.4 18.3 - - + +
234A GLN* 2.8 33.1 + - - +
235A ASP* 3.1 26.7 + - - +
236A VAL* 4.7 0.2 - - - +
237A ASP* 5.6 0.4 + - - -
460A ARG* 5.8 4.0 - - - +
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Residues in contact with THR 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A VAL* 3.7 24.8 - - + +
61A LYS* 5.5 2.0 - - - +
88A LYS* 2.9 36.1 + - - +
89A ASN* 3.9 5.5 + - - -
91A ARG* 1.3 71.7 - - - +
93A ALA* 1.3 62.4 + - - +
95A GLU* 3.5 3.3 + - - +
96A SER* 3.1 24.9 + - - -
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Residues in contact with ALA 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A VAL* 3.8 15.0 - - + +
60A LEU* 3.7 27.8 - - + -
61A LYS* 3.8 14.5 - - + +
64A ILE* 3.9 4.5 - - + -
89A ASN 3.1 20.0 + - - +
90A VAL 3.6 2.9 - - - +
92A THR* 1.3 76.4 - - - +
94A THR* 1.3 61.5 + - - +
96A SER* 2.7 25.7 + - - -
97A PHE* 3.4 10.7 - - - -
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Residues in contact with THR 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ILE* 3.7 11.2 - - - +
90A VAL* 2.7 33.3 + - - +
91A ARG* 3.7 7.4 - - - -
93A ALA* 1.3 75.0 - - - +
95A GLU* 1.3 63.1 + - - +
96A SER 3.1 4.2 + - - -
97A PHE* 3.4 15.6 + - - +
104A TYR* 3.5 30.3 - - - +
105A ARG 3.9 9.6 - - - +
107A VAL* 3.5 44.9 + - + +
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Residues in contact with GLU 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A ARG* 2.7 33.5 + - + +
92A THR* 3.9 2.9 - - - +
94A THR* 1.3 76.0 - - - +
96A SER* 1.3 56.0 + - - +
97A PHE 3.1 5.2 - - - -
98A ALA* 3.2 36.8 + - + +
99A SER 4.6 0.7 + - - -
104A TYR* 2.6 29.5 + - - -
474A LYS* 5.1 4.9 + - - -
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Residues in contact with SER 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A LYS* 3.6 29.3 - - - +
92A THR* 3.1 16.6 + - - -
93A ALA 2.7 17.2 + - - -
94A THR 3.1 0.2 - - - -
95A GLU* 1.3 76.8 - - - +
97A PHE* 1.3 71.2 + - - +
98A ALA 3.4 0.4 - - - -
99A SER* 4.4 9.4 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il